The Chemical Leak is a random side mission that appears at the Scrapyard. It can activate at any time during a campaign. The mission requires players to stand on three hexagons spread out across the scrapyard. Hordes of infested, including Stalkers and Agrons, will attack them team as they seal the containers beneath them. A player must be on each hex at all times. The completion meter will deplete quickly if a player steps off his hex.

Generally, two players should cover each hex with the last two in the middle providing fire support where needed. Sometimes it is advised for a third player to help cover the bottom hex because it is the most isolated. Alternatively, one player can cover each hex (two on the bottom one) while the rest of the team spreads out to occupy the infested and provide support where needed. Sonic Traps and Disruption Towers can help slow the hordes down.

The mission is significantly more difficult on Nightmare Mode. It is advised to skip it without a skilled and organized team. Upon completion, 8 Magazines will be airdropped to replenish those spent in the mission. This mission rewards 8 experience points (12 in Nightmare Mode), a Helium-3 Canister and 30 Credits on Normal/Hardened/Veteran or 90 Credits on Nightmare. The Chemical Leak Mission will not activate on Recruit Mode or in the Apollo Security Team Campaign.

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